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BioC 3.5: CHECK report for bioassayR on malbec2

This page was generated on 2017-08-16 13:15:19 -0400 (Wed, 16 Aug 2017).

Package 110/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioassayR 1.14.0
Tyler Backman
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/bioassayR
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: bioassayR
Version: 1.14.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings bioassayR_1.14.0.tar.gz
StartedAt: 2017-08-15 21:28:21 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:29:33 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 71.3 seconds
RetCode: 0
Status:  OK 
CheckDir: bioassayR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings bioassayR_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/bioassayR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bioassayR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bioassayR’ version ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bioassayR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

bioassayR.Rcheck/00install.out:

* installing *source* package ‘bioassayR’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘organism’ in package ‘bioassayR’
Creating a new generic function for ‘organism<-’ in package ‘bioassayR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bioassayR)

bioassayR.Rcheck/bioassayR-Ex.timings:

nameusersystemelapsed
BioAssayDB-class0.0000.0000.001
activeAgainst0.1720.0040.175
activeTargets0.0320.0000.032
addBioassayIndex0.0040.0080.011
addDataSource0.0280.0000.027
allCids0.0040.0000.004
allTargets0.0040.0000.003
assaySetTargets0.0960.0080.106
bioactivityFingerprint0.1960.0040.201
bioassay-class0.0240.0000.024
bioassaySet-class0.0000.0000.002
connectBioassayDB0.0120.0000.012
crossReactivityProbability0.2560.0040.260
disconnectBioassayDB0.0040.0080.010
dropBioassay0.1240.0000.123
dropBioassayIndex0.0120.0040.018
getAssay0.0120.0000.014
getAssays0.0400.0000.041
getBioassaySetByCids0.1200.0000.123
inactiveTargets0.0040.0000.006
loadBioassay0.1800.0040.182
loadIdMapping0.0080.0000.008
newBioassayDB0.0080.0000.006
parsePubChemBioassay0.0080.0000.009
perTargetMatrix0.1480.0000.151
queryBioassayDB0.0160.0040.017
samplebioassay0.0000.0000.002
scaleBioassaySet0.0200.0000.022
screenedAtLeast0.0040.0000.008
selectiveAgainst0.0600.0000.064
targetSelectivity0.0880.0000.091
translateTargetId0.0120.0000.009
trinarySimilarity0.1440.0000.143